Transcriptome Analyses Reveal Circadian-Related Expression Features in the Visual Systems of Two Snakes

The visual characteristics of animals with different circadian habits, especially colubrid snakes, exhibit highly variable photoreceptor morphology. While studies have reported on the diversity in retinal cell morphology among snakes with different circadian patterns, few studies have examined the expression of genes related to vision. To explore gene expression patterns in the eyes between diurnal and nocturnal snakes, we carried out RNA sequencing of six tissues (eye, heart, liver, lung, kidney, and muscle) in two colubrids with disparate circadian activities, i.e., diurnal Ahaetulla prasina and nocturnal Lycodon flavozonatum, followed by weighted gene co-expression network analysis (WGCNA). The genes in the two most correlated modules were primarily enriched in different functional pathways, thus suggesting different biological functions. Three opsin genes (RH1, LWS, and SWS) were differentially expressed between the two species. Moreover, in the phototransduction pathway, different genes were highly expressed in the eyes of both species, reflecting specific expression patterns in the eyes of snakes with different circadian activity. We also confirmed the dominance of cone- and rod-related genes in diurnal and nocturnal adaptation, respectively. This work provides an important foundation for genetic research on visual adaptation in snakes and provides further insight into the adaptive evolution of such species.

Integrative RNA-seq and ATAC-seq Analysis of Retinitis Pigmentosa Caused by PDE6 Mutation

Purpose: Inhibition of PARP1 could relieve PDE6 mutation-induced Retinitis pigmentosa (RP). However, the mechanism related with PARP1 overexpression in the RP has not been clarified. We attempted to explore the potential regulatory mechanism related with PARP1 underlying RP. Methods: ATAC-seq and RNA-seq were preformed for retina tissues of C3H and rd1 mice. The differential expressed genes (DEGs) were identified, followed by PARP1-DEG coexpression network, and PPI network construction. GO-BP and pathway enrichment of DEGs of interest were performed by clusterprofiler software. The overlapped genes that might play regulatory role in PARP1 expression were mined by integrated analysis of RNA-seq and ATAC-seq data. Results: Total 1061 DEGs were identified between C3H and rd1 group. Co-expression network was constructed with 313 PARP1-gene coexpression pairs. The down-regulated DEGs were closely related with visual perception, light stimulus related biological process, while the up-regulated DEGs were significantly enriched in phototransduction and PPAR signaling pathway. PPI network was constructed with 202 nodes and 375 edges, which was clustered into 3 modules. Module 1 genes were closely related with detection of light stimulus, visual perception related biological process and phototransduction pathway (involved with Gnat1/Guca1b/Gnat2/Sag/Pde6g). By integrated analysis of the RNA-seq and ATAC-seq, the overlapped up-regulated genes were Asxl3 and Nyap2, while the down-regulated genes were Tmem136 and Susd3. Conclusion: Gnat1 may play a key role in RP development by interacting with PARP1. Susd3 may play a regulatory role in PARP1 expression and affect RP formation.

The secrets of cryptochromes: photoreceptors, clock proteins, and magnetic sensors

A class of light-activated proteins in the eyes of birds, called cryptochromes, are thought to act as the primary magnetic sensors allowing night-migratory songbirds to navigate over thousands of kilometers using the earth’s magnetic field. Having evolved from DNA-repairing photolyases, cryptochromes have redirected the energy from light to fuel a variety of other functions: as photoreceptors, as regulators of the circadian clock – and, in some species, most likely as sensors of the magnetic field. While the quantum effects of magnetic fields on cryptochromes are already being studied in detail, almost nothing is known about the signaling cascade involving cryptochrome as the primary receptor protein. Two different screening methods have identified potential interaction partners that suggest an involvement of the visual phototransduction pathway, the visual cycle, potassium channels or glutamate receptors, but more pioneering research is needed to unravel the signaling cascade responsible for transducing the magnetic signal.

Molecular Evolution of Phototransduction Pathway Genes in Nocturnal and Diurnal Fireflies (Coleoptera: Lampyridae)

Most organisms are dependent on sensory cues from their environment for survival and reproduction. Fireflies (Coleoptera: Lampyridae) represent an ideal system for studying sensory niche adaptation due to many species relying on bioluminescent communication; as well as a diversity of ecologies. Here; using transcriptomics; we examine the phototransduction pathway in this non-model organism; and provide some of the first evidence for positive selection in the phototransduction pathway beyond opsins in beetles. Evidence for gene duplications within Lampyridae are found in inactivation no afterpotential C and inactivation no afterpotential D. We also find strong support for positive selection in arrestin-2; inactivation no afterpotential D; and transient receptor potential-like; with weak support for positive selection in guanine nucleotide-binding protein G(q) subunit alpha and neither inactivation nor afterpotential C. Taken with other recent work in flies; butterflies; and moths; this represents an exciting new avenue of study as we seek to further understand diversification and constraint on the phototransduction pathway in light of organism ecology.

Peroxisomal Multifunctional Protein 2 Deficiency Perturbs Lipid Homeostasis in the Retina and Causes Visual Dysfunction in Mice

Patients lacking multifunctional protein 2 (MFP2), the central enzyme of the peroxisomal β-oxidation pathway, develop retinopathy. This pathway is involved in the metabolism of very long chain (VLCFAs) and polyunsaturated (PUFAs) fatty acids, which are enriched in the photoreceptor outer segments (POS). The molecular mechanisms underlying the retinopathy remain, however, elusive. Here, we report that mice with MFP2 inactivation display decreased retinal function already at the age of 3 weeks, which is accompanied by a profound shortening of the photoreceptor outer and inner segments, but with preserved photoreceptor ultrastructure. Furthermore, MFP2 deficient retinas exhibit severe changes in gene expression with downregulation of genes involved in the phototransduction pathway and upregulation of inflammation related genes. Lipid profiling of the mutant retinas revealed a profound reduction of DHA-containing phospholipids. This was likely due to a hampered systemic supply and retinal traffic of this PUFA, although we cannot exclude that the local defect of peroxisomal β-oxidation contributes to this DHA decrease. Moreover, very long chain PUFAs were also reduced, with the exception of those containing ≥ 34 carbons that accumulated. The latter suggests that there is an uncontrollable elongation of retinal PUFAs. In conclusion, our data reveal that intact peroxisomal β-oxidation is indispensable for retinal integrity, most likely by maintaining PUFA homeostasis.

Evidence of Presence and Activation of the two Cell Cycle Kinases Nek6 and Nek7 in the ciliated Neuroretina

The serine/threonine NIMA kinases are widely found in eukaryotes. They are cell-cycle kinases that are associated with centrosomes and spindle apparatus and cilia. In cilia, NIMA kinases are reported to play a role in cilia length maintenance and deflagelation. Here we focus on the two Nek homologs, Nek6 and Nek7, and their potential role in retina. We report for the first-time expression of nek6 and nek7 mRNA and protein in retinal tissue. In particular, we detect localisation of these kinases to photoreceptors outer segments. Moreover, we are able to show a light-dependent phosphorylation of the activation loop (serine 206) of Nek6/7 in rod outer segments, suggesting activation of these kinases is downstream of the phototransduction pathway. Indeed, we demonstrate that Nek6/7 phosphorylation in the retina is dependent on Grk1 function. Furthermore, Nek6/7 phosphorylation can be stimulated in the brain by opiate drugs, suggesting that activation of Nek6/7 lies downstream of G protein coupled receptors activation, in general. Nek6/7 may couple photoreception with outer segment biogenesis through phosphorylation of downstream substrates, which may affect the microtubules of the axoneme.

Seminal fluid compromises visual perception in honeybee queens reducing their survival during additional mating flights

Queens of social insects make all mate-choice decisions on a single day, except in honeybees whose queens can conduct mating flights for several days even when already inseminated by a number of drones. Honeybees therefore appear to have a unique, evolutionarily derived form of sexual conflict: a queen’s decision to pursue risky additional mating flights is driven by later-life fitness gains from genetically more diverse worker-offspring but reduces paternity shares of the drones she already mated with. We used artificial insemination, RNA-sequencing and electroretinography to show that seminal fluid induces a decline in queen vision by perturbing the phototransduction pathway within 24–48 hr. Follow up field trials revealed that queens receiving seminal fluid flew two days earlier than sister queens inseminated with saline, and failed more often to return. These findings are consistent with seminal fluid components manipulating queen eyesight to reduce queen promiscuity across mating flights.

C-terminal phosphorylation regulates the kinetics of a subset of melanopsin-mediated behaviors in mice

Intrinsically photosensitive retinal ganglion cells (ipRGCs) express the photopigment melanopsin and mediate several non–image-forming visual functions, including circadian photoentrainment and the pupillary light reflex (PLR). ipRGCs act as autonomous photoreceptors via the intrinsic melanopsin-based phototransduction pathway and as a relay for rod/cone input via synaptically driven responses. Under low light intensities, where only synaptically driven rod/cone input activates ipRGCs, the duration of the ipRGC response will be determined by the termination kinetics of the rod/cone circuits. Little is known, however, about the termination kinetics of the intrinsic melanopsin-based phototransduction pathway and its contribution to several melanopsin-mediated behaviors. Here, we show that C-terminal phosphorylation of melanopsin determines the recovery kinetics of the intrinsic melanopsin-based photoresponse in ipRGCs, the duration of the PLR, and the speed of reentrainment. In contrast, circadian phase alignment and direct effects of light on activity (masking) are not influenced by C-terminal phosphorylation of melanopsin. Electrophysiological measurements demonstrate that expression of a virally encoded melanopsin lacking all C-terminal phosphorylation sites (C terminus phosphonull) leads to a prolonged intrinsic light response. In addition, mice expressing the C terminus phosphonull in ipRGCs reentrain faster to a delayed light/dark cycle compared with mice expressing virally encoded WT melanopsin; however, the phase angle of entrainment and masking were indistinguishable. Importantly, a sustained PLR in the phosphonull animals is only observed at brighter light intensities that activate melanopsin phototransduction, but not at dimmer light intensities that activate only the rod/cone pathway. Taken together, our results highlight how the kinetics of the melanopsin photoresponse differentially regulate distinct light-mediated behaviors.